Starting phenix.real_space_refine on Sun Jul 5 17:00:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ujk_64215/07_2026/9ujk_64215.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ujk_64215/07_2026/9ujk_64215.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ujk_64215/07_2026/9ujk_64215.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ujk_64215/07_2026/9ujk_64215.map" model { file = "/net/cci-nas-00/data/ceres_data/9ujk_64215/07_2026/9ujk_64215.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ujk_64215/07_2026/9ujk_64215.cif" } resolution = 2.49 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 89 5.49 5 Mg 3 5.21 5 S 70 5.16 5 C 17749 2.51 5 N 5066 2.21 5 O 5501 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28480 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1772 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 210} Chain: "B" Number of atoms: 1776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1776 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 210} Chain: "C" Number of atoms: 8783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1113, 8783 Classifications: {'peptide': 1113} Link IDs: {'PCIS': 1, 'PTRANS': 71, 'TRANS': 1040} Chain breaks: 1 Chain: "D" Number of atoms: 10753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1362, 10753 Classifications: {'peptide': 1362} Link IDs: {'PCIS': 2, 'PTRANS': 66, 'TRANS': 1293} Chain breaks: 2 Chain: "E" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 754 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain: "F" Number of atoms: 2739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2739 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 13, 'TRANS': 324} Chain breaks: 1 Chain: "G" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 881 Classifications: {'DNA': 43} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 42} Chain breaks: 1 Chain: "H" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 987 Classifications: {'DNA': 48} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 47} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 34 Unusual residues: {' MG': 2, ' ZN': 2, '1N7': 1} Classifications: {'undetermined': 5, 'water': 1} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Unresolved non-hydrogen planarities: 1 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 20156 SG CYS D1112 22.483 59.594 119.817 1.00 35.77 S ATOM 20800 SG CYS D1194 26.303 59.886 118.943 1.00 24.77 S ATOM 20856 SG CYS D1201 24.891 61.495 122.044 1.00 25.67 S ATOM 20880 SG CYS D1204 25.430 58.053 122.004 1.00 41.49 S ATOM 12800 SG CYS D 58 54.836 103.833 82.919 1.00 74.32 S ATOM 12811 SG CYS D 60 56.242 104.679 79.838 1.00 86.28 S ATOM 12922 SG CYS D 73 52.934 104.389 79.522 1.00 77.64 S ATOM 12948 SG CYS D 76 54.461 101.002 80.273 1.00 73.26 S Time building chain proxies: 5.78, per 1000 atoms: 0.20 Number of scatterers: 28480 At special positions: 0 Unit cell: (131.61, 157.29, 207.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 70 16.00 P 89 15.00 Mg 3 11.99 O 5501 8.00 N 5066 7.00 C 17749 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.16 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1601 " pdb="ZN ZN D1601 " - pdb=" SG CYS D1201 " pdb="ZN ZN D1601 " - pdb=" SG CYS D1112 " pdb="ZN ZN D1601 " - pdb=" SG CYS D1194 " pdb="ZN ZN D1601 " - pdb=" SG CYS D1204 " pdb=" ZN D1602 " pdb="ZN ZN D1602 " - pdb=" SG CYS D 73 " pdb="ZN ZN D1602 " - pdb=" SG CYS D 60 " pdb="ZN ZN D1602 " - pdb=" SG CYS D 58 " pdb="ZN ZN D1602 " - pdb=" SG CYS D 76 " Number of angles added : 12 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6214 Finding SS restraints... Secondary structure from input PDB file: 131 helices and 50 sheets defined 44.1% alpha, 17.6% beta 31 base pairs and 72 stacking pairs defined. Time for finding SS restraints: 3.08 Creating SS restraints... Processing helix chain 'A' and resid 31 through 47 Proline residue: A 39 - end of helix Processing helix chain 'A' and resid 74 through 83 Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 152 through 157 Processing helix chain 'A' and resid 206 through 223 Processing helix chain 'B' and resid 31 through 47 Proline residue: B 39 - end of helix Processing helix chain 'B' and resid 74 through 83 Processing helix chain 'B' and resid 112 through 114 No H-bonds generated for 'chain 'B' and resid 112 through 114' Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 206 through 223 Processing helix chain 'C' and resid 19 through 31 removed outlier: 3.969A pdb=" N SER C 25 " --> pdb=" O ILE C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 39 removed outlier: 3.531A pdb=" N ARG C 39 " --> pdb=" O PRO C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 52 Processing helix chain 'C' and resid 79 through 87 Processing helix chain 'C' and resid 193 through 200 Processing helix chain 'C' and resid 203 through 212 Processing helix chain 'C' and resid 217 through 222 removed outlier: 3.764A pdb=" N MET C 222 " --> pdb=" O GLN C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 228 removed outlier: 3.736A pdb=" N PHE C 227 " --> pdb=" O ASP C 223 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 223 through 228' Processing helix chain 'C' and resid 230 through 243 Processing helix chain 'C' and resid 249 through 262 Processing helix chain 'C' and resid 270 through 282 Processing helix chain 'C' and resid 302 through 316 Processing helix chain 'C' and resid 335 through 360 removed outlier: 3.556A pdb=" N LEU C 360 " --> pdb=" O ARG C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 375 through 389 removed outlier: 3.592A pdb=" N SER C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 408 removed outlier: 3.537A pdb=" N SER C 403 " --> pdb=" O ASN C 399 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 429 removed outlier: 3.529A pdb=" N ARG C 428 " --> pdb=" O GLY C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 435 removed outlier: 3.561A pdb=" N TYR C 435 " --> pdb=" O ARG C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 492 Processing helix chain 'C' and resid 525 through 529 Processing helix chain 'C' and resid 535 through 540 Processing helix chain 'C' and resid 543 through 547 Processing helix chain 'C' and resid 549 through 553 Processing helix chain 'C' and resid 554 through 565 removed outlier: 3.842A pdb=" N MET C 560 " --> pdb=" O ASN C 556 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN C 565 " --> pdb=" O GLY C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 568 No H-bonds generated for 'chain 'C' and resid 566 through 568' Processing helix chain 'C' and resid 583 through 592 removed outlier: 3.532A pdb=" N VAL C 588 " --> pdb=" O GLU C 584 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU C 592 " --> pdb=" O VAL C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 687 removed outlier: 3.857A pdb=" N ASP C 686 " --> pdb=" O ASN C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 697 Processing helix chain 'C' and resid 768 through 779 Processing helix chain 'C' and resid 854 through 858 removed outlier: 3.583A pdb=" N MET C 858 " --> pdb=" O VAL C 855 " (cutoff:3.500A) Processing helix chain 'C' and resid 874 through 880 removed outlier: 4.721A pdb=" N SER C 878 " --> pdb=" O LEU C 874 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG C 879 " --> pdb=" O GLY C 875 " (cutoff:3.500A) Processing helix chain 'C' and resid 882 through 898 removed outlier: 3.503A pdb=" N PHE C 896 " --> pdb=" O LEU C 892 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 933 removed outlier: 4.296A pdb=" N ARG C 929 " --> pdb=" O TYR C 925 " (cutoff:3.500A) Processing helix chain 'C' and resid 937 through 950 removed outlier: 3.533A pdb=" N LYS C 949 " --> pdb=" O ARG C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 969 removed outlier: 3.529A pdb=" N GLN C 969 " --> pdb=" O GLU C 965 " (cutoff:3.500A) Processing helix chain 'C' and resid 1000 through 1004 Processing helix chain 'C' and resid 1023 through 1027 Processing helix chain 'C' and resid 1033 through 1044 Processing helix chain 'C' and resid 1045 through 1054 Processing helix chain 'C' and resid 1059 through 1072 Processing helix chain 'C' and resid 1082 through 1094 removed outlier: 3.618A pdb=" N ARG C1086 " --> pdb=" O PRO C1082 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 21 Processing helix chain 'D' and resid 46 through 51 Processing helix chain 'D' and resid 65 through 69 Processing helix chain 'D' and resid 82 through 88 removed outlier: 3.554A pdb=" N VAL D 85 " --> pdb=" O LYS D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 107 removed outlier: 3.570A pdb=" N ASP D 107 " --> pdb=" O TRP D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 117 Processing helix chain 'D' and resid 119 through 128 Processing helix chain 'D' and resid 154 through 164 Processing helix chain 'D' and resid 372 through 376 Processing helix chain 'D' and resid 456 through 468 removed outlier: 3.808A pdb=" N ALA D 460 " --> pdb=" O MET D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 481 Processing helix chain 'D' and resid 485 through 506 Processing helix chain 'D' and resid 508 through 511 Processing helix chain 'D' and resid 521 through 525 Processing helix chain 'D' and resid 538 through 560 removed outlier: 4.146A pdb=" N ASP D 542 " --> pdb=" O SER D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 583 Processing helix chain 'D' and resid 602 through 608 Processing helix chain 'D' and resid 612 through 618 Processing helix chain 'D' and resid 646 through 653 removed outlier: 3.526A pdb=" N GLU D 651 " --> pdb=" O ARG D 647 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 664 Processing helix chain 'D' and resid 669 through 679 removed outlier: 4.018A pdb=" N ARG D 679 " --> pdb=" O ARG D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 680 through 683 Processing helix chain 'D' and resid 685 through 695 removed outlier: 3.789A pdb=" N ASP D 689 " --> pdb=" O ASP D 685 " (cutoff:3.500A) Processing helix chain 'D' and resid 709 through 711 No H-bonds generated for 'chain 'D' and resid 709 through 711' Processing helix chain 'D' and resid 729 through 731 No H-bonds generated for 'chain 'D' and resid 729 through 731' Processing helix chain 'D' and resid 732 through 737 Processing helix chain 'D' and resid 752 through 762 Processing helix chain 'D' and resid 764 through 768 Processing helix chain 'D' and resid 782 through 794 removed outlier: 3.552A pdb=" N ILE D 792 " --> pdb=" O GLY D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 808 through 818 Processing helix chain 'D' and resid 835 through 841 Processing helix chain 'D' and resid 845 through 855 Processing helix chain 'D' and resid 876 through 891 Processing helix chain 'D' and resid 892 through 900 removed outlier: 3.591A pdb=" N GLU D 898 " --> pdb=" O LYS D 894 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE D 900 " --> pdb=" O ALA D 896 " (cutoff:3.500A) Processing helix chain 'D' and resid 907 through 923 Processing helix chain 'D' and resid 923 through 946 removed outlier: 3.595A pdb=" N THR D 944 " --> pdb=" O THR D 940 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLY D 946 " --> pdb=" O SER D 942 " (cutoff:3.500A) Processing helix chain 'D' and resid 950 through 954 Processing helix chain 'D' and resid 958 through 980 removed outlier: 4.029A pdb=" N GLN D 962 " --> pdb=" O GLU D 958 " (cutoff:3.500A) Processing helix chain 'D' and resid 984 through 1015 Processing helix chain 'D' and resid 1018 through 1026 Processing helix chain 'D' and resid 1031 through 1040 Processing helix chain 'D' and resid 1066 through 1103 removed outlier: 3.737A pdb=" N HIS D1075 " --> pdb=" O PHE D1071 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLY D1076 " --> pdb=" O ILE D1072 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA D1089 " --> pdb=" O ALA D1085 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASP D1090 " --> pdb=" O LEU D1086 " (cutoff:3.500A) Processing helix chain 'D' and resid 1136 through 1145 Processing helix chain 'D' and resid 1167 through 1180 Processing helix chain 'D' and resid 1202 through 1206 Processing helix chain 'D' and resid 1220 through 1231 Processing helix chain 'D' and resid 1232 through 1236 Processing helix chain 'D' and resid 1255 through 1264 Processing helix chain 'D' and resid 1331 through 1339 Processing helix chain 'D' and resid 1340 through 1359 removed outlier: 3.714A pdb=" N VAL D1355 " --> pdb=" O GLU D1351 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR D1356 " --> pdb=" O ILE D1352 " (cutoff:3.500A) Processing helix chain 'D' and resid 1364 through 1376 removed outlier: 4.079A pdb=" N ILE D1368 " --> pdb=" O HIS D1364 " (cutoff:3.500A) Processing helix chain 'D' and resid 1397 through 1410 removed outlier: 3.527A pdb=" N GLU D1410 " --> pdb=" O ARG D1406 " (cutoff:3.500A) Processing helix chain 'D' and resid 1423 through 1430 Processing helix chain 'D' and resid 1433 through 1439 Processing helix chain 'D' and resid 1442 through 1454 Processing helix chain 'D' and resid 1461 through 1469 removed outlier: 4.070A pdb=" N ASN D1465 " --> pdb=" O GLY D1461 " (cutoff:3.500A) Processing helix chain 'D' and resid 1474 through 1478 Processing helix chain 'D' and resid 1489 through 1500 Processing helix chain 'E' and resid 5 through 11 Processing helix chain 'E' and resid 15 through 33 removed outlier: 3.602A pdb=" N LEU E 19 " --> pdb=" O SER E 15 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR E 20 " --> pdb=" O LYS E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 71 removed outlier: 3.706A pdb=" N GLY E 71 " --> pdb=" O GLU E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 93 Processing helix chain 'F' and resid 79 through 89 Processing helix chain 'F' and resid 95 through 121 Processing helix chain 'F' and resid 123 through 137 Processing helix chain 'F' and resid 152 through 165 Processing helix chain 'F' and resid 167 through 190 removed outlier: 4.328A pdb=" N TYR F 173 " --> pdb=" O GLU F 169 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU F 174 " --> pdb=" O HIS F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 200 removed outlier: 3.774A pdb=" N VAL F 195 " --> pdb=" O ASN F 191 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL F 196 " --> pdb=" O LEU F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 203 No H-bonds generated for 'chain 'F' and resid 201 through 203' Processing helix chain 'F' and resid 208 through 227 Processing helix chain 'F' and resid 228 through 232 removed outlier: 3.637A pdb=" N ARG F 231 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 255 removed outlier: 3.720A pdb=" N TYR F 238 " --> pdb=" O LYS F 234 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TRP F 241 " --> pdb=" O THR F 237 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TRP F 242 " --> pdb=" O TYR F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 283 Processing helix chain 'F' and resid 287 through 296 Processing helix chain 'F' and resid 300 through 311 Processing helix chain 'F' and resid 328 through 333 removed outlier: 3.663A pdb=" N ILE F 333 " --> pdb=" O GLY F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 360 removed outlier: 3.797A pdb=" N LYS F 360 " --> pdb=" O LYS F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 373 removed outlier: 3.626A pdb=" N MET F 367 " --> pdb=" O GLU F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 391 Processing helix chain 'F' and resid 393 through 416 Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 16 removed outlier: 6.124A pdb=" N ASP A 193 " --> pdb=" O PRO A 27 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 104 removed outlier: 3.521A pdb=" N SER A 55 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ASP A 145 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL A 53 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N GLY A 147 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N THR A 51 " --> pdb=" O GLY A 147 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 89 Processing sheet with id=AA4, first strand: chain 'A' and resid 107 through 110 removed outlier: 6.641A pdb=" N LYS A 107 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N THR A 131 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL A 109 " --> pdb=" O ILE A 129 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 150 through 151 Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 16 removed outlier: 3.688A pdb=" N TYR B 20 " --> pdb=" O GLN B 16 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASP B 193 " --> pdb=" O PRO B 27 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N THR B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU B 186 " --> pdb=" O THR B 190 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 104 removed outlier: 3.678A pdb=" N SER B 55 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASP B 145 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N VAL B 53 " --> pdb=" O ASP B 145 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLY B 147 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N THR B 51 " --> pdb=" O GLY B 147 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 87 through 89 Processing sheet with id=AA9, first strand: chain 'B' and resid 108 through 110 removed outlier: 6.864A pdb=" N VAL B 109 " --> pdb=" O ILE B 129 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 150 through 151 Processing sheet with id=AB2, first strand: chain 'C' and resid 2 through 5 Processing sheet with id=AB3, first strand: chain 'C' and resid 54 through 55 removed outlier: 5.534A pdb=" N LEU C 66 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ILE C 101 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N PHE C 68 " --> pdb=" O GLN C 99 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLN C 99 " --> pdb=" O PHE C 68 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU C 70 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ALA C 96 " --> pdb=" O PHE C 114 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N PHE C 114 " --> pdb=" O ALA C 96 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU C 98 " --> pdb=" O GLU C 112 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N GLU C 112 " --> pdb=" O LEU C 98 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N LEU C 100 " --> pdb=" O GLU C 110 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N GLU C 110 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N HIS C 102 " --> pdb=" O ILE C 108 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE C 108 " --> pdb=" O HIS C 102 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 127 through 129 Processing sheet with id=AB5, first strand: chain 'C' and resid 331 through 334 removed outlier: 6.377A pdb=" N SER C 138 " --> pdb=" O SER C 411 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 145 through 150 removed outlier: 6.633A pdb=" N TYR C 158 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N VAL C 176 " --> pdb=" O TYR C 158 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 291 through 294 Processing sheet with id=AB8, first strand: chain 'C' and resid 460 through 461 removed outlier: 5.441A pdb=" N GLU C 482 " --> pdb=" O ARG C 473 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL C 475 " --> pdb=" O THR C 480 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N THR C 480 " --> pdb=" O VAL C 475 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 460 through 461 Processing sheet with id=AC1, first strand: chain 'C' and resid 503 through 504 removed outlier: 3.655A pdb=" N ARG C 507 " --> pdb=" O GLU C 504 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 595 through 596 removed outlier: 6.390A pdb=" N LEU C 595 " --> pdb=" O LEU C 655 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 620 through 624 removed outlier: 6.877A pdb=" N ARG C 610 " --> pdb=" O VAL C 606 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N VAL C 606 " --> pdb=" O ARG C 610 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL C 612 " --> pdb=" O ALA C 604 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 629 through 630 Processing sheet with id=AC5, first strand: chain 'C' and resid 661 through 662 Processing sheet with id=AC6, first strand: chain 'C' and resid 971 through 972 removed outlier: 6.843A pdb=" N ILE C 688 " --> pdb=" O LYS C 851 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N LEU C 853 " --> pdb=" O ILE C 688 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE C 690 " --> pdb=" O LEU C 853 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL C 689 " --> pdb=" O ILE C 870 " (cutoff:3.500A) removed outlier: 8.834A pdb=" N VAL C 869 " --> pdb=" O ASN C 671 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU C 673 " --> pdb=" O VAL C 869 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N LEU C 871 " --> pdb=" O LEU C 673 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ALA C 675 " --> pdb=" O LEU C 871 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL C 988 " --> pdb=" O ILE C 676 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 702 through 713 removed outlier: 3.588A pdb=" N ARG C 802 " --> pdb=" O TYR C 826 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ALA C 828 " --> pdb=" O VAL C 800 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N VAL C 800 " --> pdb=" O ALA C 828 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N LYS C 830 " --> pdb=" O GLY C 798 " (cutoff:3.500A) removed outlier: 9.259A pdb=" N GLY C 798 " --> pdb=" O LYS C 830 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 721 through 722 Processing sheet with id=AC9, first strand: chain 'C' and resid 754 through 756 removed outlier: 6.699A pdb=" N LEU C 790 " --> pdb=" O LEU C 755 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1006 through 1008 removed outlier: 6.478A pdb=" N CYS D 642 " --> pdb=" O VAL D 719 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL D 721 " --> pdb=" O CYS D 642 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LEU D 644 " --> pdb=" O VAL D 721 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1030 through 1032 removed outlier: 3.633A pdb=" N GLN C1030 " --> pdb=" O VAL D 623 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1097 through 1102 Processing sheet with id=AD4, first strand: chain 'D' and resid 22 through 25 removed outlier: 7.638A pdb=" N HIS D 92 " --> pdb=" O TYR D 23 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLU D 25 " --> pdb=" O HIS D 92 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N GLU D 94 " --> pdb=" O GLU D 25 " (cutoff:3.500A) removed outlier: 10.147A pdb=" N LEU D 95 " --> pdb=" O PRO D 518 " (cutoff:3.500A) removed outlier: 10.676A pdb=" N THR D 97 " --> pdb=" O ALA D 516 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ALA D 516 " --> pdb=" O THR D 97 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 71 through 72 removed outlier: 4.143A pdb=" N LYS D 71 " --> pdb=" O VAL D 80 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 152 through 153 removed outlier: 6.652A pdb=" N ASP D 453 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 141 through 142 Processing sheet with id=AD8, first strand: chain 'D' and resid 166 through 170 removed outlier: 3.839A pdb=" N GLU D 183 " --> pdb=" O ALA D 203 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 344 through 346 removed outlier: 7.095A pdb=" N GLU D 389 " --> pdb=" O ARG D 209 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL D 211 " --> pdb=" O LEU D 387 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU D 387 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL D 213 " --> pdb=" O VAL D 385 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL D 385 " --> pdb=" O VAL D 213 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TYR D 215 " --> pdb=" O GLY D 383 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLY D 383 " --> pdb=" O TYR D 215 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA D 359 " --> pdb=" O VAL D 385 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 351 through 353 Processing sheet with id=AE2, first strand: chain 'D' and resid 398 through 402 removed outlier: 3.593A pdb=" N GLY D 433 " --> pdb=" O VAL D 415 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP D 413 " --> pdb=" O VAL D 435 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 420 through 422 removed outlier: 7.148A pdb=" N VAL D 427 " --> pdb=" O LEU D 421 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 527 through 529 removed outlier: 6.676A pdb=" N PHE D 535 " --> pdb=" O VAL F 315 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 827 through 828 Processing sheet with id=AE6, first strand: chain 'D' and resid 842 through 843 Processing sheet with id=AE7, first strand: chain 'D' and resid 1106 through 1109 Processing sheet with id=AE8, first strand: chain 'D' and resid 1118 through 1121 Processing sheet with id=AE9, first strand: chain 'D' and resid 1123 through 1126 Processing sheet with id=AF1, first strand: chain 'D' and resid 1153 through 1155 Processing sheet with id=AF2, first strand: chain 'D' and resid 1300 through 1305 removed outlier: 4.198A pdb=" N LEU D1290 " --> pdb=" O LEU D1305 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 1394 through 1396 removed outlier: 4.515A pdb=" N TYR D1378 " --> pdb=" O LEU D1420 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ALA D1416 " --> pdb=" O THR D1382 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 1485 through 1488 Processing sheet with id=AF5, first strand: chain 'E' and resid 47 through 49 1250 hydrogen bonds defined for protein. 3477 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 73 hydrogen bonds 146 hydrogen bond angles 0 basepair planarities 31 basepair parallelities 72 stacking parallelities Total time for adding SS restraints: 8.30 Time building geometry restraints manager: 2.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4692 1.31 - 1.43: 7477 1.43 - 1.56: 16698 1.56 - 1.69: 181 1.69 - 1.81: 127 Bond restraints: 29175 Sorted by residual: bond pdb=" C3' DA H 7 " pdb=" C2' DA H 7 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C3' DA G 27 " pdb=" C2' DA G 27 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DG H 4 " pdb=" C2' DG H 4 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.00e+01 bond pdb=" C3' DT G 31 " pdb=" C2' DT G 31 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.91e+00 bond pdb=" C3' DC G 28 " pdb=" C2' DC G 28 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.73e+00 ... (remaining 29170 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.19: 38552 1.19 - 2.38: 998 2.38 - 3.57: 267 3.57 - 4.77: 29 4.77 - 5.96: 3 Bond angle restraints: 39849 Sorted by residual: angle pdb=" N3 DT G 39 " pdb=" C4 DT G 39 " pdb=" O4 DT G 39 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT G 40 " pdb=" C4 DT G 40 " pdb=" O4 DT G 40 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT H 30 " pdb=" C4 DT H 30 " pdb=" O4 DT H 30 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.70e+01 angle pdb=" N3 DT G 4 " pdb=" C4 DT G 4 " pdb=" O4 DT G 4 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 angle pdb=" N3 DT G 42 " pdb=" C4 DT G 42 " pdb=" O4 DT G 42 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.66e+01 ... (remaining 39844 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.79: 16266 19.79 - 39.58: 1070 39.58 - 59.37: 359 59.37 - 79.16: 54 79.16 - 98.94: 15 Dihedral angle restraints: 17764 sinusoidal: 8109 harmonic: 9655 Sorted by residual: dihedral pdb=" CA TYR D1207 " pdb=" C TYR D1207 " pdb=" N ASP D1208 " pdb=" CA ASP D1208 " ideal model delta harmonic sigma weight residual 180.00 150.78 29.22 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA SER A 46 " pdb=" C SER A 46 " pdb=" N SER A 47 " pdb=" CA SER A 47 " ideal model delta harmonic sigma weight residual -180.00 -161.90 -18.10 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA SER D 782 " pdb=" C SER D 782 " pdb=" N ARG D 783 " pdb=" CA ARG D 783 " ideal model delta harmonic sigma weight residual -180.00 -162.68 -17.32 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 17761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 3388 0.043 - 0.085: 749 0.085 - 0.127: 346 0.127 - 0.170: 8 0.170 - 0.212: 2 Chirality restraints: 4493 Sorted by residual: chirality pdb=" C20 1N7 D1605 " pdb=" C21 1N7 D1605 " pdb=" C22 1N7 D1605 " pdb=" C9 1N7 D1605 " both_signs ideal model delta sigma weight residual False 2.59 2.80 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA ILE F 260 " pdb=" N ILE F 260 " pdb=" C ILE F 260 " pdb=" CB ILE F 260 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.98e-01 chirality pdb=" CA ARG F 259 " pdb=" N ARG F 259 " pdb=" C ARG F 259 " pdb=" CB ARG F 259 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.29e-01 ... (remaining 4490 not shown) Planarity restraints: 4893 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP D 743 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.03e+00 pdb=" CG ASP D 743 " 0.035 2.00e-02 2.50e+03 pdb=" OD1 ASP D 743 " -0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP D 743 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D1207 " 0.020 2.00e-02 2.50e+03 1.31e-02 3.42e+00 pdb=" CG TYR D1207 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR D1207 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR D1207 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR D1207 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR D1207 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR D1207 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR D1207 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL D 145 " -0.027 5.00e-02 4.00e+02 4.08e-02 2.66e+00 pdb=" N PRO D 146 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 146 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 146 " -0.023 5.00e-02 4.00e+02 ... (remaining 4890 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 255 2.63 - 3.19: 24776 3.19 - 3.76: 43600 3.76 - 4.33: 65959 4.33 - 4.90: 105776 Nonbonded interactions: 240366 Sorted by model distance: nonbonded pdb="MG MG D1603 " pdb=" O HOH D1701 " model vdw 2.057 2.170 nonbonded pdb=" OD1 ASP D 741 " pdb="MG MG D1603 " model vdw 2.057 2.170 nonbonded pdb=" OD1 ASP D 739 " pdb="MG MG D1603 " model vdw 2.126 2.170 nonbonded pdb=" OD1 ASP D 743 " pdb="MG MG D1603 " model vdw 2.141 2.170 nonbonded pdb=" O GLU C 55 " pdb=" NH1 ARG C 356 " model vdw 2.197 3.120 ... (remaining 240361 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 229) selection = (chain 'B' and resid 6 through 229) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.05 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 31.960 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 29183 Z= 0.235 Angle : 0.518 17.258 39861 Z= 0.337 Chirality : 0.042 0.212 4493 Planarity : 0.003 0.041 4893 Dihedral : 14.899 98.944 11550 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.14), residues: 3336 helix: 1.04 (0.15), residues: 1273 sheet: 0.30 (0.24), residues: 460 loop : 0.39 (0.15), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 589 TYR 0.031 0.001 TYR D1207 PHE 0.019 0.001 PHE C 699 TRP 0.010 0.001 TRP B 200 HIS 0.006 0.001 HIS C 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.24 (29175) covalent geometry : angle 0.49239 / 0.34 (39849) hydrogen bonds : bond 0.21305 / 14.19 ( 1321) hydrogen bonds : angle 7.29535 / 4.99 ( 3623) metal coordination : bond 0.01322 / 0.68 ( 8) metal coordination : angle 9.26174 / 4.30 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 353 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 179 VAL cc_start: 0.8582 (t) cc_final: 0.7865 (m) REVERT: D 483 HIS cc_start: 0.8117 (t-90) cc_final: 0.7836 (t-90) outliers start: 0 outliers final: 0 residues processed: 353 average time/residue: 1.0035 time to fit residues: 394.1405 Evaluate side-chains 185 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.3980 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.1980 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 6.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 139 ASN C 538 GLN C 829 GLN D 388 HIS ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 HIS F 269 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.092305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.062137 restraints weight = 52083.812| |-----------------------------------------------------------------------------| r_work (start): 0.2730 rms_B_bonded: 2.35 r_work: 0.2580 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2449 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2449 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2546 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2546 r_free = 0.2546 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2546 r_free = 0.2546 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2546 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 29183 Z= 0.182 Angle : 0.607 8.430 39861 Z= 0.327 Chirality : 0.045 0.170 4493 Planarity : 0.005 0.058 4893 Dihedral : 15.346 81.235 4799 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.19 % Allowed : 6.92 % Favored : 91.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.14), residues: 3336 helix: 1.49 (0.14), residues: 1296 sheet: 0.30 (0.24), residues: 451 loop : 0.47 (0.16), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 416 TYR 0.019 0.001 TYR D1207 PHE 0.017 0.002 PHE A 179 TRP 0.012 0.001 TRP B 200 HIS 0.006 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 (29175) covalent geometry : angle 0.60360 / 0.33 (39849) hydrogen bonds : bond 0.05684 / 3.84 ( 1321) hydrogen bonds : angle 5.08574 / 3.51 ( 3623) metal coordination : bond 0.00549 / 0.23 ( 8) metal coordination : angle 3.71222 / 1.87 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 195 time to evaluate : 1.145 Fit side-chains revert: symmetry clash REVERT: A 108 GLU cc_start: 0.8990 (OUTLIER) cc_final: 0.8396 (mp0) REVERT: A 154 GLU cc_start: 0.8522 (pm20) cc_final: 0.8292 (pm20) REVERT: A 155 LYS cc_start: 0.8762 (mtpp) cc_final: 0.8454 (ttmt) REVERT: A 185 ARG cc_start: 0.9142 (OUTLIER) cc_final: 0.8652 (ttm-80) REVERT: B 185 ARG cc_start: 0.8247 (ptt90) cc_final: 0.7879 (ptm-80) REVERT: C 154 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7788 (ptm-80) REVERT: C 159 ILE cc_start: 0.8619 (pt) cc_final: 0.8412 (mp) REVERT: C 216 GLU cc_start: 0.8219 (pm20) cc_final: 0.7222 (tm-30) REVERT: C 229 MET cc_start: 0.7704 (ttp) cc_final: 0.7429 (ttp) REVERT: C 233 GLU cc_start: 0.9034 (mp0) cc_final: 0.8801 (pt0) REVERT: C 357 GLU cc_start: 0.8208 (tp30) cc_final: 0.7895 (tp30) REVERT: C 361 MET cc_start: 0.7884 (pp-130) cc_final: 0.7643 (pp-130) REVERT: C 384 GLU cc_start: 0.8340 (tp30) cc_final: 0.7921 (mm-30) REVERT: C 420 ARG cc_start: 0.8010 (ttp80) cc_final: 0.7718 (tmm-80) REVERT: C 771 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7710 (tm-30) REVERT: C 775 ARG cc_start: 0.8566 (mtp85) cc_final: 0.8214 (mmt90) REVERT: D 124 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8269 (tp30) REVERT: D 190 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7863 (tp30) REVERT: D 386 HIS cc_start: 0.7772 (m-70) cc_final: 0.7380 (m170) REVERT: E 88 GLU cc_start: 0.8818 (tp30) cc_final: 0.8521 (tp30) REVERT: F 419 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8282 (tpp80) outliers start: 34 outliers final: 7 residues processed: 217 average time/residue: 0.8998 time to fit residues: 220.4222 Evaluate side-chains 188 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 175 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain B residue 16 GLN Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 901 GLN Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain F residue 419 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 259 optimal weight: 0.7980 chunk 246 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 323 optimal weight: 0.3980 chunk 93 optimal weight: 4.9990 chunk 195 optimal weight: 0.6980 chunk 186 optimal weight: 10.0000 chunk 4 optimal weight: 0.9990 chunk 202 optimal weight: 6.9990 chunk 15 optimal weight: 0.0000 chunk 7 optimal weight: 0.7980 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 670 GLN ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.092824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.062693 restraints weight = 51617.181| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 2.35 r_work: 0.2605 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2475 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2475 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2567 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2567 r_free = 0.2567 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2567 r_free = 0.2567 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2567 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 29183 Z= 0.114 Angle : 0.524 9.818 39861 Z= 0.282 Chirality : 0.042 0.145 4493 Planarity : 0.004 0.065 4893 Dihedral : 15.335 82.603 4799 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.15 % Allowed : 8.29 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.14), residues: 3336 helix: 1.63 (0.14), residues: 1314 sheet: 0.38 (0.24), residues: 446 loop : 0.43 (0.16), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 67 TYR 0.013 0.001 TYR D1207 PHE 0.013 0.001 PHE D 740 TRP 0.011 0.001 TRP B 200 HIS 0.005 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (29175) covalent geometry : angle 0.52231 / 0.28 (39849) hydrogen bonds : bond 0.04409 / 2.98 ( 1321) hydrogen bonds : angle 4.62421 / 3.21 ( 3623) metal coordination : bond 0.00291 / 0.11 ( 8) metal coordination : angle 2.43931 / 1.25 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 201 time to evaluate : 1.063 Fit side-chains REVERT: A 108 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.8383 (mp0) REVERT: A 154 GLU cc_start: 0.8592 (pm20) cc_final: 0.8319 (pm20) REVERT: A 155 LYS cc_start: 0.8688 (mtpp) cc_final: 0.8382 (ttmt) REVERT: A 185 ARG cc_start: 0.9135 (OUTLIER) cc_final: 0.8752 (ttm-80) REVERT: B 183 ASP cc_start: 0.8785 (OUTLIER) cc_final: 0.8371 (t0) REVERT: B 185 ARG cc_start: 0.8313 (ptt90) cc_final: 0.7907 (ptm-80) REVERT: C 154 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7665 (ptm-80) REVERT: C 216 GLU cc_start: 0.8220 (pm20) cc_final: 0.7246 (tm-30) REVERT: C 229 MET cc_start: 0.7741 (ttp) cc_final: 0.7503 (ttp) REVERT: C 230 ARG cc_start: 0.8137 (ttm110) cc_final: 0.7854 (ttm110) REVERT: C 233 GLU cc_start: 0.9102 (mp0) cc_final: 0.8874 (pt0) REVERT: C 357 GLU cc_start: 0.8377 (tp30) cc_final: 0.8019 (tp30) REVERT: C 361 MET cc_start: 0.7964 (pp-130) cc_final: 0.7541 (pp-130) REVERT: C 384 GLU cc_start: 0.8362 (tp30) cc_final: 0.7921 (mm-30) REVERT: C 420 ARG cc_start: 0.7970 (ttp80) cc_final: 0.7699 (tmm-80) REVERT: C 771 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7643 (tm-30) REVERT: C 775 ARG cc_start: 0.8569 (mtp85) cc_final: 0.8196 (mmt90) REVERT: D 65 ARG cc_start: 0.7512 (mmm160) cc_final: 0.6963 (mpt-90) REVERT: D 67 ARG cc_start: 0.7918 (ptm160) cc_final: 0.7349 (ptp-170) REVERT: D 124 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8190 (tp30) REVERT: D 366 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7805 (tptm) REVERT: D 386 HIS cc_start: 0.8074 (m-70) cc_final: 0.7817 (m-70) REVERT: D 763 MET cc_start: 0.9424 (mtp) cc_final: 0.9205 (mtm) REVERT: D 1124 GLN cc_start: 0.8427 (tt0) cc_final: 0.8194 (tt0) REVERT: D 1337 GLU cc_start: 0.7919 (pp20) cc_final: 0.7651 (pp20) REVERT: E 88 GLU cc_start: 0.8788 (tp30) cc_final: 0.8398 (tp30) REVERT: F 285 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8405 (mm-30) REVERT: F 419 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.8336 (tpp80) outliers start: 33 outliers final: 5 residues processed: 221 average time/residue: 0.8686 time to fit residues: 217.2857 Evaluate side-chains 192 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 180 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain B residue 16 GLN Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 366 LYS Chi-restraints excluded: chain D residue 597 ASP Chi-restraints excluded: chain D residue 648 MET Chi-restraints excluded: chain D residue 1313 VAL Chi-restraints excluded: chain D residue 1452 ILE Chi-restraints excluded: chain F residue 419 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 216 optimal weight: 3.9990 chunk 238 optimal weight: 0.6980 chunk 263 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 chunk 91 optimal weight: 0.8980 chunk 169 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 197 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 139 ASN C 999 HIS E 86 GLN ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.089398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.059038 restraints weight = 51380.117| |-----------------------------------------------------------------------------| r_work (start): 0.2680 rms_B_bonded: 2.34 r_work: 0.2525 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2393 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2393 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2490 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2490 r_free = 0.2490 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2490 r_free = 0.2490 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2490 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 29183 Z= 0.179 Angle : 0.547 9.799 39861 Z= 0.292 Chirality : 0.043 0.150 4493 Planarity : 0.005 0.093 4893 Dihedral : 15.359 78.776 4799 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.15 % Allowed : 9.06 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.14), residues: 3336 helix: 1.74 (0.14), residues: 1311 sheet: 0.33 (0.24), residues: 461 loop : 0.47 (0.16), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 8 TYR 0.016 0.001 TYR D 345 PHE 0.016 0.001 PHE A 179 TRP 0.011 0.001 TRP A 200 HIS 0.007 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (29175) covalent geometry : angle 0.54554 / 0.29 (39849) hydrogen bonds : bond 0.04521 / 3.06 ( 1321) hydrogen bonds : angle 4.49930 / 3.12 ( 3623) metal coordination : bond 0.00545 / 0.26 ( 8) metal coordination : angle 2.52188 / 1.23 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 190 time to evaluate : 0.802 Fit side-chains REVERT: A 108 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8500 (mp0) REVERT: A 110 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7509 (mtpp) REVERT: A 154 GLU cc_start: 0.8684 (pm20) cc_final: 0.8370 (pm20) REVERT: A 155 LYS cc_start: 0.8715 (mtpp) cc_final: 0.8401 (ttmt) REVERT: A 185 ARG cc_start: 0.9126 (ptm-80) cc_final: 0.8711 (ttm-80) REVERT: B 91 ASN cc_start: 0.8264 (t0) cc_final: 0.7970 (t0) REVERT: B 185 ARG cc_start: 0.8465 (ptt90) cc_final: 0.8031 (ptm-80) REVERT: C 154 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7220 (ptm-80) REVERT: C 229 MET cc_start: 0.7802 (OUTLIER) cc_final: 0.7237 (ttp) REVERT: C 233 GLU cc_start: 0.9122 (mp0) cc_final: 0.8884 (pt0) REVERT: C 237 ARG cc_start: 0.8751 (tpp80) cc_final: 0.8518 (ttt90) REVERT: C 353 ARG cc_start: 0.8018 (mtp85) cc_final: 0.7680 (mtm-85) REVERT: C 357 GLU cc_start: 0.8337 (tp30) cc_final: 0.7972 (tp30) REVERT: C 361 MET cc_start: 0.8035 (pp-130) cc_final: 0.7587 (pp-130) REVERT: C 384 GLU cc_start: 0.8410 (tp30) cc_final: 0.7969 (mm-30) REVERT: C 420 ARG cc_start: 0.8111 (ttp80) cc_final: 0.7849 (tmm-80) REVERT: C 771 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7701 (tm-30) REVERT: C 775 ARG cc_start: 0.8463 (mtp85) cc_final: 0.8115 (mmt90) REVERT: C 1000 MET cc_start: 0.8594 (mtt) cc_final: 0.8208 (mtt) REVERT: D 67 ARG cc_start: 0.7855 (ptm160) cc_final: 0.7316 (ptp-170) REVERT: D 124 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8305 (tp30) REVERT: D 190 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7941 (tp30) REVERT: D 345 TYR cc_start: 0.7108 (m-10) cc_final: 0.6893 (m-10) REVERT: D 366 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7908 (tptm) REVERT: D 386 HIS cc_start: 0.7986 (m-70) cc_final: 0.7690 (m-70) REVERT: D 420 VAL cc_start: 0.9125 (OUTLIER) cc_final: 0.8920 (t) REVERT: D 594 PRO cc_start: 0.9031 (Cg_exo) cc_final: 0.8818 (Cg_endo) REVERT: D 1013 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8356 (mp0) REVERT: D 1100 ASP cc_start: 0.8394 (OUTLIER) cc_final: 0.8006 (m-30) REVERT: D 1124 GLN cc_start: 0.8445 (tt0) cc_final: 0.8191 (tt0) REVERT: E 88 GLU cc_start: 0.8855 (tp30) cc_final: 0.8425 (tp30) REVERT: F 410 TYR cc_start: 0.8435 (t80) cc_final: 0.7898 (t80) outliers start: 33 outliers final: 9 residues processed: 212 average time/residue: 0.8443 time to fit residues: 202.8789 Evaluate side-chains 193 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 174 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 486 MET Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 366 LYS Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 597 ASP Chi-restraints excluded: chain D residue 782 SER Chi-restraints excluded: chain D residue 972 LEU Chi-restraints excluded: chain D residue 1013 GLU Chi-restraints excluded: chain D residue 1100 ASP Chi-restraints excluded: chain D residue 1312 LEU Chi-restraints excluded: chain D residue 1452 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 109 optimal weight: 3.9990 chunk 326 optimal weight: 5.9990 chunk 320 optimal weight: 5.9990 chunk 268 optimal weight: 0.1980 chunk 63 optimal weight: 0.7980 chunk 315 optimal weight: 3.9990 chunk 171 optimal weight: 8.9990 chunk 284 optimal weight: 6.9990 chunk 115 optimal weight: 0.0570 chunk 22 optimal weight: 6.9990 chunk 173 optimal weight: 0.0060 overall best weight: 1.0116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 163 ASN ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.090229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.059991 restraints weight = 51548.861| |-----------------------------------------------------------------------------| r_work (start): 0.2699 rms_B_bonded: 2.34 r_work: 0.2545 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2412 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2412 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2506 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2506 r_free = 0.2506 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2506 r_free = 0.2506 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2506 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29183 Z= 0.127 Angle : 0.503 9.024 39861 Z= 0.271 Chirality : 0.042 0.145 4493 Planarity : 0.004 0.068 4893 Dihedral : 15.304 78.590 4799 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.84 % Allowed : 9.76 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.15), residues: 3336 helix: 1.79 (0.14), residues: 1319 sheet: 0.36 (0.24), residues: 460 loop : 0.50 (0.16), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG D 65 TYR 0.012 0.001 TYR D 989 PHE 0.010 0.001 PHE B 179 TRP 0.011 0.001 TRP B 200 HIS 0.005 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (29175) covalent geometry : angle 0.50145 / 0.27 (39849) hydrogen bonds : bond 0.04020 / 2.71 ( 1321) hydrogen bonds : angle 4.36296 / 3.04 ( 3623) metal coordination : bond 0.00319 / 0.15 ( 8) metal coordination : angle 2.08341 / 1.02 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 191 time to evaluate : 1.128 Fit side-chains REVERT: A 108 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8507 (mp0) REVERT: A 110 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7469 (mtpp) REVERT: A 145 ASP cc_start: 0.8783 (m-30) cc_final: 0.8449 (m-30) REVERT: A 154 GLU cc_start: 0.8724 (pm20) cc_final: 0.8418 (pm20) REVERT: A 155 LYS cc_start: 0.8706 (mtpp) cc_final: 0.8375 (ttmt) REVERT: A 185 ARG cc_start: 0.9119 (ptm-80) cc_final: 0.8696 (ttm-80) REVERT: B 91 ASN cc_start: 0.8298 (t0) cc_final: 0.7993 (t0) REVERT: B 185 ARG cc_start: 0.8597 (ptt90) cc_final: 0.8162 (ptm-80) REVERT: B 190 THR cc_start: 0.8763 (p) cc_final: 0.8485 (t) REVERT: C 154 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7330 (ptm-80) REVERT: C 229 MET cc_start: 0.7810 (ttp) cc_final: 0.7257 (ttp) REVERT: C 230 ARG cc_start: 0.8229 (ttm110) cc_final: 0.7632 (ttm110) REVERT: C 233 GLU cc_start: 0.9128 (mp0) cc_final: 0.8857 (pt0) REVERT: C 237 ARG cc_start: 0.8761 (tpp80) cc_final: 0.8503 (ttt90) REVERT: C 353 ARG cc_start: 0.8037 (mtp85) cc_final: 0.7812 (ttm-80) REVERT: C 357 GLU cc_start: 0.8337 (tp30) cc_final: 0.7971 (tp30) REVERT: C 361 MET cc_start: 0.8085 (pp-130) cc_final: 0.7574 (pp-130) REVERT: C 384 GLU cc_start: 0.8399 (tp30) cc_final: 0.7953 (mm-30) REVERT: C 420 ARG cc_start: 0.8102 (ttp80) cc_final: 0.7836 (tmm-80) REVERT: C 771 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7706 (tm-30) REVERT: C 775 ARG cc_start: 0.8441 (mtp85) cc_final: 0.8214 (mmt90) REVERT: C 1000 MET cc_start: 0.8665 (mtt) cc_final: 0.8351 (mtt) REVERT: D 65 ARG cc_start: 0.7548 (mmm160) cc_final: 0.6994 (mpt-90) REVERT: D 68 PHE cc_start: 0.7315 (m-80) cc_final: 0.7012 (m-80) REVERT: D 124 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8291 (tp30) REVERT: D 190 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7986 (tp30) REVERT: D 345 TYR cc_start: 0.7128 (m-10) cc_final: 0.6892 (m-10) REVERT: D 351 MET cc_start: 0.8966 (OUTLIER) cc_final: 0.8745 (mpp) REVERT: D 366 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.7906 (tptm) REVERT: D 386 HIS cc_start: 0.8063 (m-70) cc_final: 0.7817 (m-70) REVERT: D 420 VAL cc_start: 0.9115 (OUTLIER) cc_final: 0.8913 (t) REVERT: D 594 PRO cc_start: 0.9015 (Cg_exo) cc_final: 0.8797 (Cg_endo) REVERT: D 763 MET cc_start: 0.9492 (mtp) cc_final: 0.9269 (mtm) REVERT: D 1013 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8337 (mp0) REVERT: D 1124 GLN cc_start: 0.8447 (tt0) cc_final: 0.8197 (tt0) REVERT: E 44 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8491 (mt-10) REVERT: E 88 GLU cc_start: 0.8845 (tp30) cc_final: 0.8357 (tp30) REVERT: F 379 ARG cc_start: 0.7306 (ttm110) cc_final: 0.7006 (ttm110) REVERT: F 410 TYR cc_start: 0.8432 (t80) cc_final: 0.7892 (t80) outliers start: 24 outliers final: 6 residues processed: 208 average time/residue: 0.8931 time to fit residues: 210.3569 Evaluate side-chains 195 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 180 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 557 ARG Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 351 MET Chi-restraints excluded: chain D residue 366 LYS Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 597 ASP Chi-restraints excluded: chain D residue 692 GLU Chi-restraints excluded: chain D residue 782 SER Chi-restraints excluded: chain D residue 1013 GLU Chi-restraints excluded: chain D residue 1312 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 109 optimal weight: 6.9990 chunk 287 optimal weight: 0.8980 chunk 8 optimal weight: 0.3980 chunk 194 optimal weight: 0.0670 chunk 106 optimal weight: 2.9990 chunk 193 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 326 optimal weight: 6.9990 chunk 219 optimal weight: 5.9990 chunk 156 optimal weight: 0.8980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 139 ASN ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.091358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.061344 restraints weight = 51768.345| |-----------------------------------------------------------------------------| r_work (start): 0.2719 rms_B_bonded: 2.33 r_work: 0.2566 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2433 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2433 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2526 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2526 r_free = 0.2526 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2526 r_free = 0.2526 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2526 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 29183 Z= 0.106 Angle : 0.488 8.798 39861 Z= 0.264 Chirality : 0.041 0.142 4493 Planarity : 0.004 0.074 4893 Dihedral : 15.226 77.074 4799 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.98 % Allowed : 9.79 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.15), residues: 3336 helix: 1.89 (0.14), residues: 1319 sheet: 0.37 (0.24), residues: 453 loop : 0.55 (0.16), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 8 TYR 0.012 0.001 TYR D 989 PHE 0.010 0.001 PHE C 922 TRP 0.011 0.001 TRP B 200 HIS 0.005 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (29175) covalent geometry : angle 0.48743 / 0.26 (39849) hydrogen bonds : bond 0.03651 / 2.46 ( 1321) hydrogen bonds : angle 4.23604 / 2.96 ( 3623) metal coordination : bond 0.00266 / 0.12 ( 8) metal coordination : angle 1.88621 / 0.94 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 188 time to evaluate : 0.940 Fit side-chains REVERT: A 110 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7462 (mtpp) REVERT: A 145 ASP cc_start: 0.8838 (m-30) cc_final: 0.8540 (m-30) REVERT: A 154 GLU cc_start: 0.8748 (pm20) cc_final: 0.8439 (pm20) REVERT: A 155 LYS cc_start: 0.8704 (mtpp) cc_final: 0.8377 (ttmt) REVERT: A 185 ARG cc_start: 0.9084 (OUTLIER) cc_final: 0.8728 (ttm-80) REVERT: B 7 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8541 (pptt) REVERT: B 91 ASN cc_start: 0.8339 (t0) cc_final: 0.8024 (t0) REVERT: B 102 LYS cc_start: 0.8707 (mmmt) cc_final: 0.8186 (mmmt) REVERT: B 139 ASN cc_start: 0.8723 (t0) cc_final: 0.8521 (t0) REVERT: B 183 ASP cc_start: 0.8839 (OUTLIER) cc_final: 0.8414 (t0) REVERT: B 185 ARG cc_start: 0.8653 (ptt90) cc_final: 0.8220 (ptm-80) REVERT: B 190 THR cc_start: 0.8752 (p) cc_final: 0.8484 (t) REVERT: C 154 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7380 (ptm-80) REVERT: C 216 GLU cc_start: 0.8243 (pm20) cc_final: 0.8039 (pm20) REVERT: C 229 MET cc_start: 0.7856 (ttp) cc_final: 0.7287 (ttp) REVERT: C 230 ARG cc_start: 0.8273 (ttm110) cc_final: 0.7670 (ttm110) REVERT: C 233 GLU cc_start: 0.9134 (mp0) cc_final: 0.8849 (pt0) REVERT: C 237 ARG cc_start: 0.8757 (tpp80) cc_final: 0.8505 (ttt90) REVERT: C 353 ARG cc_start: 0.8005 (mtp85) cc_final: 0.7801 (ttm-80) REVERT: C 357 GLU cc_start: 0.8305 (tp30) cc_final: 0.7971 (tp30) REVERT: C 361 MET cc_start: 0.8140 (pp-130) cc_final: 0.7623 (pp-130) REVERT: C 384 GLU cc_start: 0.8390 (tp30) cc_final: 0.7906 (mm-30) REVERT: C 419 THR cc_start: 0.9098 (m) cc_final: 0.8665 (p) REVERT: C 420 ARG cc_start: 0.8081 (ttp80) cc_final: 0.7855 (tmm-80) REVERT: C 771 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7718 (tm-30) REVERT: C 775 ARG cc_start: 0.8408 (mtp85) cc_final: 0.8185 (mmt90) REVERT: C 1000 MET cc_start: 0.8575 (mtt) cc_final: 0.8372 (mtt) REVERT: C 1052 MET cc_start: 0.9154 (OUTLIER) cc_final: 0.8850 (mmm) REVERT: D 65 ARG cc_start: 0.7516 (mmm160) cc_final: 0.6885 (mmt180) REVERT: D 67 ARG cc_start: 0.7899 (tmm-80) cc_final: 0.7571 (tmm-80) REVERT: D 124 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8284 (tp30) REVERT: D 190 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8061 (tp30) REVERT: D 345 TYR cc_start: 0.7174 (m-10) cc_final: 0.6913 (m-10) REVERT: D 351 MET cc_start: 0.8963 (OUTLIER) cc_final: 0.8692 (mpp) REVERT: D 366 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.7949 (tptm) REVERT: D 386 HIS cc_start: 0.7989 (m-70) cc_final: 0.7728 (m-70) REVERT: D 420 VAL cc_start: 0.9107 (OUTLIER) cc_final: 0.8904 (t) REVERT: D 594 PRO cc_start: 0.9037 (Cg_exo) cc_final: 0.8808 (Cg_endo) REVERT: D 763 MET cc_start: 0.9459 (mtp) cc_final: 0.9253 (mtm) REVERT: D 1013 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8354 (mp0) REVERT: D 1124 GLN cc_start: 0.8431 (tt0) cc_final: 0.8190 (tt0) REVERT: E 44 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8466 (mt-10) REVERT: E 88 GLU cc_start: 0.8840 (tp30) cc_final: 0.8310 (tp30) REVERT: F 410 TYR cc_start: 0.8458 (t80) cc_final: 0.7896 (t80) outliers start: 28 outliers final: 6 residues processed: 207 average time/residue: 0.8578 time to fit residues: 201.5081 Evaluate side-chains 194 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 176 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 557 ARG Chi-restraints excluded: chain C residue 1052 MET Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 351 MET Chi-restraints excluded: chain D residue 366 LYS Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 597 ASP Chi-restraints excluded: chain D residue 692 GLU Chi-restraints excluded: chain D residue 782 SER Chi-restraints excluded: chain D residue 1013 GLU Chi-restraints excluded: chain D residue 1452 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 111 optimal weight: 3.9990 chunk 308 optimal weight: 0.0970 chunk 150 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 148 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 49 optimal weight: 8.9990 chunk 181 optimal weight: 8.9990 chunk 266 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 overall best weight: 2.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 163 ASN C 130 ASN D 762 GLN ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 381 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.087547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.057105 restraints weight = 52076.577| |-----------------------------------------------------------------------------| r_work (start): 0.2753 rms_B_bonded: 2.35 r_work: 0.2618 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2496 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2536 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2536 r_free = 0.2536 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2536 r_free = 0.2536 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2536 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 29183 Z= 0.228 Angle : 0.558 9.245 39861 Z= 0.294 Chirality : 0.044 0.149 4493 Planarity : 0.005 0.101 4893 Dihedral : 15.307 77.005 4799 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.87 % Allowed : 10.38 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.14), residues: 3336 helix: 1.83 (0.14), residues: 1311 sheet: 0.29 (0.24), residues: 462 loop : 0.55 (0.16), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 198 TYR 0.014 0.001 TYR D 128 PHE 0.018 0.002 PHE A 179 TRP 0.012 0.001 TRP D1398 HIS 0.007 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.23 (29175) covalent geometry : angle 0.55598 / 0.29 (39849) hydrogen bonds : bond 0.04521 / 3.05 ( 1321) hydrogen bonds : angle 4.38213 / 3.05 ( 3623) metal coordination : bond 0.00705 / 0.36 ( 8) metal coordination : angle 2.70215 / 1.29 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 184 time to evaluate : 1.120 Fit side-chains revert: symmetry clash REVERT: A 110 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.7620 (mtpp) REVERT: A 145 ASP cc_start: 0.8898 (m-30) cc_final: 0.8543 (m-30) REVERT: A 154 GLU cc_start: 0.8817 (pm20) cc_final: 0.8504 (pm20) REVERT: A 155 LYS cc_start: 0.8846 (mtpp) cc_final: 0.8509 (ttmt) REVERT: B 7 LYS cc_start: 0.8987 (OUTLIER) cc_final: 0.8643 (pptt) REVERT: B 91 ASN cc_start: 0.8505 (t0) cc_final: 0.8190 (t0) REVERT: B 102 LYS cc_start: 0.8748 (mmmt) cc_final: 0.8118 (mmmt) REVERT: B 139 ASN cc_start: 0.8737 (t0) cc_final: 0.8471 (t0) REVERT: B 185 ARG cc_start: 0.8651 (ptt90) cc_final: 0.8016 (ptm-80) REVERT: B 190 THR cc_start: 0.8737 (p) cc_final: 0.8460 (t) REVERT: C 154 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7266 (ptm-80) REVERT: C 229 MET cc_start: 0.7929 (ttp) cc_final: 0.7478 (ttp) REVERT: C 230 ARG cc_start: 0.8310 (ttm110) cc_final: 0.7700 (ttp-110) REVERT: C 233 GLU cc_start: 0.9150 (mp0) cc_final: 0.8836 (pt0) REVERT: C 237 ARG cc_start: 0.8815 (tpp80) cc_final: 0.8559 (ttt90) REVERT: C 353 ARG cc_start: 0.8136 (mtp85) cc_final: 0.7911 (ttm-80) REVERT: C 357 GLU cc_start: 0.8425 (tp30) cc_final: 0.8083 (tp30) REVERT: C 361 MET cc_start: 0.8217 (pp-130) cc_final: 0.7661 (pp-130) REVERT: C 384 GLU cc_start: 0.8506 (tp30) cc_final: 0.8068 (mm-30) REVERT: C 420 ARG cc_start: 0.8168 (ttp80) cc_final: 0.7878 (tmm-80) REVERT: C 771 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7788 (tm-30) REVERT: C 775 ARG cc_start: 0.8512 (mtp85) cc_final: 0.8258 (mmt90) REVERT: C 1052 MET cc_start: 0.9204 (mtt) cc_final: 0.8821 (mmm) REVERT: D 124 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8527 (tp30) REVERT: D 190 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8104 (tp30) REVERT: D 345 TYR cc_start: 0.7484 (m-10) cc_final: 0.7185 (m-10) REVERT: D 351 MET cc_start: 0.9074 (OUTLIER) cc_final: 0.8837 (mpp) REVERT: D 365 ASP cc_start: 0.7709 (m-30) cc_final: 0.7363 (m-30) REVERT: D 366 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8063 (tptm) REVERT: D 386 HIS cc_start: 0.8059 (m-70) cc_final: 0.7783 (m-70) REVERT: D 420 VAL cc_start: 0.9142 (OUTLIER) cc_final: 0.8885 (t) REVERT: D 594 PRO cc_start: 0.9006 (Cg_exo) cc_final: 0.8788 (Cg_endo) REVERT: D 1013 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8406 (mp0) REVERT: D 1100 ASP cc_start: 0.8454 (OUTLIER) cc_final: 0.8068 (m-30) REVERT: D 1124 GLN cc_start: 0.8535 (tt0) cc_final: 0.8276 (tt0) REVERT: E 44 GLU cc_start: 0.8947 (mt-10) cc_final: 0.8669 (mt-10) REVERT: E 88 GLU cc_start: 0.8927 (tp30) cc_final: 0.8519 (tp30) REVERT: F 410 TYR cc_start: 0.8481 (t80) cc_final: 0.7904 (t80) REVERT: F 422 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8166 (tp) outliers start: 25 outliers final: 7 residues processed: 201 average time/residue: 0.8344 time to fit residues: 190.3744 Evaluate side-chains 197 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 179 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 557 ARG Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 351 MET Chi-restraints excluded: chain D residue 366 LYS Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 597 ASP Chi-restraints excluded: chain D residue 782 SER Chi-restraints excluded: chain D residue 1013 GLU Chi-restraints excluded: chain D residue 1100 ASP Chi-restraints excluded: chain D residue 1452 ILE Chi-restraints excluded: chain F residue 422 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 142 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 329 optimal weight: 10.0000 chunk 222 optimal weight: 0.7980 chunk 306 optimal weight: 9.9990 chunk 187 optimal weight: 4.9990 chunk 213 optimal weight: 2.9990 chunk 210 optimal weight: 2.9990 chunk 298 optimal weight: 1.9990 chunk 175 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 179 ASN ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.088337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.058037 restraints weight = 52083.093| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 2.33 r_work: 0.2636 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2516 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2516 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2501 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2501 r_free = 0.2501 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2501 r_free = 0.2501 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2501 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 29183 Z= 0.152 Angle : 0.516 8.806 39861 Z= 0.275 Chirality : 0.042 0.147 4493 Planarity : 0.004 0.051 4893 Dihedral : 15.279 75.851 4799 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.84 % Allowed : 10.59 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.15), residues: 3336 helix: 1.88 (0.14), residues: 1313 sheet: 0.31 (0.24), residues: 461 loop : 0.56 (0.16), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 65 TYR 0.013 0.001 TYR D 989 PHE 0.017 0.001 PHE D 68 TRP 0.012 0.001 TRP B 200 HIS 0.005 0.001 HIS B 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (29175) covalent geometry : angle 0.51460 / 0.28 (39849) hydrogen bonds : bond 0.04002 / 2.70 ( 1321) hydrogen bonds : angle 4.28182 / 2.98 ( 3623) metal coordination : bond 0.00514 / 0.26 ( 8) metal coordination : angle 2.35338 / 1.11 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 183 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.7618 (mtpp) REVERT: A 145 ASP cc_start: 0.8871 (m-30) cc_final: 0.8549 (m-30) REVERT: A 154 GLU cc_start: 0.8831 (pm20) cc_final: 0.8516 (pm20) REVERT: A 155 LYS cc_start: 0.8868 (mtpp) cc_final: 0.8534 (ttmt) REVERT: A 227 ASN cc_start: 0.9184 (m110) cc_final: 0.8888 (m110) REVERT: B 7 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8662 (pptt) REVERT: B 91 ASN cc_start: 0.8574 (t0) cc_final: 0.8258 (t0) REVERT: B 102 LYS cc_start: 0.8816 (mmmt) cc_final: 0.8172 (mmmt) REVERT: B 185 ARG cc_start: 0.8661 (ptt90) cc_final: 0.8035 (ptm-80) REVERT: B 190 THR cc_start: 0.8691 (p) cc_final: 0.8432 (t) REVERT: C 154 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7272 (ptm-80) REVERT: C 229 MET cc_start: 0.8029 (ttp) cc_final: 0.7595 (ttp) REVERT: C 230 ARG cc_start: 0.8335 (ttm110) cc_final: 0.7726 (ttp-110) REVERT: C 233 GLU cc_start: 0.9162 (mp0) cc_final: 0.8847 (pt0) REVERT: C 237 ARG cc_start: 0.8817 (tpp80) cc_final: 0.8568 (ttt90) REVERT: C 353 ARG cc_start: 0.8141 (mtp85) cc_final: 0.7928 (ttm-80) REVERT: C 357 GLU cc_start: 0.8433 (tp30) cc_final: 0.8100 (tp30) REVERT: C 361 MET cc_start: 0.8214 (pp-130) cc_final: 0.7651 (pp-130) REVERT: C 384 GLU cc_start: 0.8491 (tp30) cc_final: 0.8059 (mm-30) REVERT: C 1000 MET cc_start: 0.8739 (mtt) cc_final: 0.8213 (mtt) REVERT: D 65 ARG cc_start: 0.7627 (mmm160) cc_final: 0.6952 (mpt-90) REVERT: D 124 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8510 (tp30) REVERT: D 190 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8102 (tp30) REVERT: D 351 MET cc_start: 0.9099 (OUTLIER) cc_final: 0.8800 (mpp) REVERT: D 366 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8070 (tptm) REVERT: D 386 HIS cc_start: 0.8084 (m-70) cc_final: 0.7806 (m-70) REVERT: D 420 VAL cc_start: 0.9107 (OUTLIER) cc_final: 0.8859 (t) REVERT: D 594 PRO cc_start: 0.9053 (Cg_exo) cc_final: 0.8851 (Cg_endo) REVERT: D 1013 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8425 (mp0) REVERT: D 1124 GLN cc_start: 0.8541 (tt0) cc_final: 0.8282 (tt0) REVERT: E 44 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8671 (mt-10) REVERT: E 88 GLU cc_start: 0.8945 (tp30) cc_final: 0.8531 (tp30) REVERT: F 410 TYR cc_start: 0.8474 (t80) cc_final: 0.7898 (t80) REVERT: F 422 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8164 (mt) outliers start: 24 outliers final: 10 residues processed: 199 average time/residue: 0.8921 time to fit residues: 200.5358 Evaluate side-chains 192 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 172 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 557 ARG Chi-restraints excluded: chain C residue 928 LYS Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 351 MET Chi-restraints excluded: chain D residue 366 LYS Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 597 ASP Chi-restraints excluded: chain D residue 692 GLU Chi-restraints excluded: chain D residue 782 SER Chi-restraints excluded: chain D residue 1013 GLU Chi-restraints excluded: chain D residue 1452 ILE Chi-restraints excluded: chain F residue 422 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 121 optimal weight: 2.9990 chunk 223 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 88 optimal weight: 0.0980 chunk 20 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 261 optimal weight: 0.9980 chunk 285 optimal weight: 4.9990 chunk 79 optimal weight: 8.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.088173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.057838 restraints weight = 52029.728| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 2.33 r_work: 0.2619 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2498 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2498 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2570 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2570 r_free = 0.2570 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2569 r_free = 0.2569 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2569 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 29183 Z= 0.163 Angle : 0.524 8.646 39861 Z= 0.279 Chirality : 0.043 0.149 4493 Planarity : 0.005 0.104 4893 Dihedral : 15.278 75.006 4799 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.73 % Allowed : 10.94 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.15), residues: 3336 helix: 1.89 (0.14), residues: 1313 sheet: 0.32 (0.24), residues: 461 loop : 0.56 (0.16), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG D 198 TYR 0.012 0.001 TYR D 989 PHE 0.013 0.001 PHE D 68 TRP 0.012 0.001 TRP B 200 HIS 0.006 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 (29175) covalent geometry : angle 0.52287 / 0.28 (39849) hydrogen bonds : bond 0.04051 / 2.73 ( 1321) hydrogen bonds : angle 4.27559 / 2.98 ( 3623) metal coordination : bond 0.00513 / 0.26 ( 8) metal coordination : angle 2.24691 / 1.07 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 175 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.7578 (mtpp) REVERT: A 145 ASP cc_start: 0.8857 (m-30) cc_final: 0.8506 (m-30) REVERT: A 154 GLU cc_start: 0.8830 (pm20) cc_final: 0.8511 (pm20) REVERT: A 155 LYS cc_start: 0.8845 (mtpp) cc_final: 0.8510 (ttmt) REVERT: A 227 ASN cc_start: 0.9151 (m110) cc_final: 0.8872 (m110) REVERT: B 7 LYS cc_start: 0.9029 (OUTLIER) cc_final: 0.8677 (pptt) REVERT: B 91 ASN cc_start: 0.8572 (t0) cc_final: 0.8253 (t0) REVERT: B 185 ARG cc_start: 0.8671 (ptt90) cc_final: 0.8035 (ptm-80) REVERT: B 190 THR cc_start: 0.8673 (p) cc_final: 0.8414 (t) REVERT: C 154 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.7176 (ptm-80) REVERT: C 229 MET cc_start: 0.8001 (ttp) cc_final: 0.7555 (ttp) REVERT: C 230 ARG cc_start: 0.8332 (ttm110) cc_final: 0.7747 (ttp-110) REVERT: C 233 GLU cc_start: 0.9164 (mp0) cc_final: 0.8860 (pt0) REVERT: C 237 ARG cc_start: 0.8798 (tpp80) cc_final: 0.8551 (ttt90) REVERT: C 353 ARG cc_start: 0.8065 (mtp85) cc_final: 0.7862 (ttm-80) REVERT: C 357 GLU cc_start: 0.8417 (tp30) cc_final: 0.8088 (tp30) REVERT: C 361 MET cc_start: 0.8210 (pp-130) cc_final: 0.7646 (pp-130) REVERT: C 384 GLU cc_start: 0.8473 (tp30) cc_final: 0.8032 (mm-30) REVERT: C 420 ARG cc_start: 0.8424 (ttm110) cc_final: 0.8220 (tmm-80) REVERT: C 1000 MET cc_start: 0.8756 (mtt) cc_final: 0.8352 (mtt) REVERT: C 1052 MET cc_start: 0.9188 (OUTLIER) cc_final: 0.8879 (mmm) REVERT: D 65 ARG cc_start: 0.7597 (mmm160) cc_final: 0.6948 (mpt-90) REVERT: D 124 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8481 (tp30) REVERT: D 190 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8202 (tp30) REVERT: D 351 MET cc_start: 0.9075 (OUTLIER) cc_final: 0.8848 (mpp) REVERT: D 366 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8096 (tptm) REVERT: D 386 HIS cc_start: 0.8026 (m-70) cc_final: 0.7759 (m-70) REVERT: D 420 VAL cc_start: 0.9050 (OUTLIER) cc_final: 0.8803 (t) REVERT: D 1013 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8418 (mp0) REVERT: D 1100 ASP cc_start: 0.8430 (OUTLIER) cc_final: 0.8070 (m-30) REVERT: D 1124 GLN cc_start: 0.8506 (tt0) cc_final: 0.8251 (tt0) REVERT: E 44 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8652 (mt-10) REVERT: E 88 GLU cc_start: 0.8918 (tp30) cc_final: 0.8518 (tp30) REVERT: F 410 TYR cc_start: 0.8467 (t80) cc_final: 0.7885 (t80) REVERT: F 422 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8275 (mt) outliers start: 21 outliers final: 10 residues processed: 190 average time/residue: 0.8963 time to fit residues: 193.3194 Evaluate side-chains 191 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 169 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 557 ARG Chi-restraints excluded: chain C residue 928 LYS Chi-restraints excluded: chain C residue 1052 MET Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 351 MET Chi-restraints excluded: chain D residue 366 LYS Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 597 ASP Chi-restraints excluded: chain D residue 782 SER Chi-restraints excluded: chain D residue 1013 GLU Chi-restraints excluded: chain D residue 1100 ASP Chi-restraints excluded: chain D residue 1452 ILE Chi-restraints excluded: chain F residue 422 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 276 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 253 optimal weight: 4.9990 chunk 296 optimal weight: 0.5980 chunk 338 optimal weight: 20.0000 chunk 281 optimal weight: 6.9990 chunk 261 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 128 optimal weight: 0.7980 chunk 232 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.089182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.058971 restraints weight = 51592.732| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 2.32 r_work: 0.2665 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2543 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2522 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2522 r_free = 0.2522 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2522 r_free = 0.2522 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2522 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 29183 Z= 0.108 Angle : 0.509 9.127 39861 Z= 0.270 Chirality : 0.042 0.145 4493 Planarity : 0.004 0.079 4893 Dihedral : 15.231 73.748 4799 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.63 % Allowed : 11.15 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.15), residues: 3336 helix: 1.93 (0.14), residues: 1319 sheet: 0.31 (0.25), residues: 451 loop : 0.57 (0.16), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG D1499 TYR 0.012 0.001 TYR D 989 PHE 0.018 0.001 PHE D 68 TRP 0.012 0.001 TRP B 200 HIS 0.005 0.001 HIS B 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (29175) covalent geometry : angle 0.50739 / 0.27 (39849) hydrogen bonds : bond 0.03644 / 2.45 ( 1321) hydrogen bonds : angle 4.18115 / 2.92 ( 3623) metal coordination : bond 0.00330 / 0.16 ( 8) metal coordination : angle 2.12214 / 1.01 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 182 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.7603 (mtpp) REVERT: A 145 ASP cc_start: 0.8806 (m-30) cc_final: 0.8482 (m-30) REVERT: A 154 GLU cc_start: 0.8830 (pm20) cc_final: 0.8522 (pm20) REVERT: A 155 LYS cc_start: 0.8867 (mtpp) cc_final: 0.8539 (ttmt) REVERT: A 227 ASN cc_start: 0.9201 (m110) cc_final: 0.8936 (m110) REVERT: B 91 ASN cc_start: 0.8619 (t0) cc_final: 0.8302 (t0) REVERT: B 185 ARG cc_start: 0.8680 (ptt90) cc_final: 0.8068 (ptm-80) REVERT: B 190 THR cc_start: 0.8615 (p) cc_final: 0.8354 (t) REVERT: C 154 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7300 (ptm-80) REVERT: C 229 MET cc_start: 0.8058 (ttp) cc_final: 0.7823 (ttp) REVERT: C 230 ARG cc_start: 0.8382 (ttm110) cc_final: 0.7822 (ttp-110) REVERT: C 233 GLU cc_start: 0.9165 (mp0) cc_final: 0.8875 (pt0) REVERT: C 353 ARG cc_start: 0.8073 (mtp85) cc_final: 0.7872 (ttm-80) REVERT: C 357 GLU cc_start: 0.8405 (tp30) cc_final: 0.8101 (tp30) REVERT: C 361 MET cc_start: 0.8215 (pp-130) cc_final: 0.7646 (pp-130) REVERT: C 384 GLU cc_start: 0.8505 (tp30) cc_final: 0.8042 (mm-30) REVERT: C 420 ARG cc_start: 0.8391 (ttm110) cc_final: 0.8176 (tmm-80) REVERT: C 723 THR cc_start: 0.9152 (t) cc_final: 0.8864 (p) REVERT: C 1000 MET cc_start: 0.8719 (mtt) cc_final: 0.8264 (mtt) REVERT: D 65 ARG cc_start: 0.7584 (mmm160) cc_final: 0.7344 (mmm160) REVERT: D 124 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8485 (tp30) REVERT: D 190 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8198 (tp30) REVERT: D 351 MET cc_start: 0.9089 (OUTLIER) cc_final: 0.8793 (mpp) REVERT: D 366 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8169 (tptm) REVERT: D 386 HIS cc_start: 0.8041 (m-70) cc_final: 0.7805 (m-70) REVERT: D 420 VAL cc_start: 0.9075 (OUTLIER) cc_final: 0.8855 (t) REVERT: D 483 HIS cc_start: 0.7695 (t-90) cc_final: 0.7338 (t-90) REVERT: D 1013 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8399 (mp0) REVERT: D 1100 ASP cc_start: 0.8391 (OUTLIER) cc_final: 0.8000 (m-30) REVERT: D 1124 GLN cc_start: 0.8525 (tt0) cc_final: 0.8289 (tt0) REVERT: E 44 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8629 (mt-10) REVERT: E 88 GLU cc_start: 0.8923 (tp30) cc_final: 0.8514 (tp30) REVERT: F 410 TYR cc_start: 0.8462 (t80) cc_final: 0.7935 (t80) REVERT: F 422 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8393 (mt) outliers start: 18 outliers final: 7 residues processed: 195 average time/residue: 0.9757 time to fit residues: 216.7082 Evaluate side-chains 192 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 175 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 557 ARG Chi-restraints excluded: chain C residue 928 LYS Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 351 MET Chi-restraints excluded: chain D residue 366 LYS Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 597 ASP Chi-restraints excluded: chain D residue 782 SER Chi-restraints excluded: chain D residue 1013 GLU Chi-restraints excluded: chain D residue 1100 ASP Chi-restraints excluded: chain D residue 1452 ILE Chi-restraints excluded: chain F residue 422 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 6 optimal weight: 4.9990 chunk 165 optimal weight: 2.9990 chunk 169 optimal weight: 0.9980 chunk 160 optimal weight: 0.5980 chunk 33 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 129 optimal weight: 0.6980 chunk 89 optimal weight: 5.9990 chunk 116 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 GLN ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.088240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.057938 restraints weight = 51884.510| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 2.32 r_work: 0.2626 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2505 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2573 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2573 r_free = 0.2573 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2573 r_free = 0.2573 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2573 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 29183 Z= 0.164 Angle : 0.526 8.549 39861 Z= 0.278 Chirality : 0.042 0.148 4493 Planarity : 0.005 0.113 4893 Dihedral : 15.248 73.487 4799 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.70 % Allowed : 11.19 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.15), residues: 3336 helix: 1.94 (0.14), residues: 1313 sheet: 0.30 (0.25), residues: 458 loop : 0.59 (0.16), residues: 1565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG D1499 TYR 0.012 0.001 TYR D 989 PHE 0.013 0.001 PHE D1008 TRP 0.012 0.001 TRP D1398 HIS 0.006 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 (29175) covalent geometry : angle 0.52453 / 0.28 (39849) hydrogen bonds : bond 0.03951 / 2.66 ( 1321) hydrogen bonds : angle 4.21895 / 2.94 ( 3623) metal coordination : bond 0.00501 / 0.25 ( 8) metal coordination : angle 2.20503 / 1.06 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11546.48 seconds wall clock time: 196 minutes 32.85 seconds (11792.85 seconds total)